Hi Greg, Thank you very much. Now i know how to do it and where to look.
Regards, Evgueni 2008/8/8 Greg Landrum <[email protected]> > Yes, as Igor suggests, calling DGeomHelpers::EmbedMolecule will > generate a set of 3D coordinates for the molecule. > > The conformations that one gets from EmbedMolecule aren't particularly > nice looking, so if you'd like the 3D coordinates to be a little > nicer, try cleaning them up: > > ForceFields::ForceField *ff=UFF::constructForceField(*mol); > ff->initialize(); > int res=1; > while res { > res=ff->minimize(); > } > delete ff; > > If you'd rather have 2D coordinates for the molecules, do this instead: > RDDepict::compute2DCoords(*mol) > > Best Regards, > -greg > > > On Fri, Aug 8, 2008 at 2:10 PM, Igor Filippov <[email protected]> > wrote: > > Add this on top: > > DGeomHelpers::EmbedMolecule(*mol); > > > > Igor > > > > On Fri, 2008-08-08 at 13:07 +0100, Evgueni Kolossov wrote: > >> Thanks - this is kind of works. > >> Unfortunately there is no atomic coordinates generated - how we can do > >> this? Otherwise it will display just single dot. > >> > >> Regards, > >> Evgueni > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- Dr. Evgueni Kolossov (PhD) [email protected] Tel. +44(0)1628 627168 Mob. +44(0)7812070446
